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I don't see why Samus should want the Galactic Federation to accept here. Basically they are doing whatever they want, and it is very corrupt. Breeding metroid's, and using X parasites that are very very dangerous, aren't something that she is for, and it doesn't make them look anything near good. Also at this point in the story, space pirates aren't as much as a threat as they were in games that take place earlier in the time line. There is no point to risk populations by breeding metroid's or use X parasites. Also how is having more options make it hard to choose on expanding the story? Imo it makes it much easier than say being restricted so much that there is only one option that leaves out most or all plot holes. Evidence of having few options is the split timeline theory made by Nintendo, after tons of plot holes in the serious were recognized. I doubt that Nintendo thought of it beforehand. Before that Zelda stories, were actually pretty great. After that everything became complex, and not even Nintendo can make sense of it.